# Contributing Welcome to `fhirpack` contributor\'s guide. This document focuses on getting any potential contributor familiarized with the development processes, but [other kinds of contributions](https://opensource.guide/how-to-contribute) are also appreciated. If you are new to using [git](https://git-scm.com) or have never collaborated in a project previously, please have a look at [contribution-guide.org](https://www.contribution-guide.org/). Other resources are also listed in the excellent [guide created by FreeCodeCamp](https://github.com/FreeCodeCamp/how-to-contribute-to-open-source)[^1]. Please notice, all users and contributors are expected to be **open, considerate, reasonable, and respectful**. When in doubt, [Python Software Foundation\'s Code of Conduct](https://www.python.org/psf/conduct/) is a good reference in terms of behavior guidelines. Issue Reports ------------- If you experience bugs or general issues with `fhirpack`, please have a look on the [issue tracker](https://github.com/%3CUSERNAME%3E/fhirpack/issues). If you don\'t see anything useful there, please feel free to fire an issue report. ```{tip} Please don\'t forget to include the closed issues in your search. Sometimes a solution was already reported, and the problem is considered **solved**. ``` New issue reports should include information about your programming environment (e.g., operating system, Python version) and steps to reproduce the problem. Please try also to simplify the reproduction steps to a very minimal example that still illustrates the problem you are facing. By removing other factors, you help us to identify the root cause of the issue. Documentation Improvements -------------------------- You can help improve `fhirpack` docs by making them more readable and coherent, or by adding missing information and correcting mistakes. `fhirpack` documentation uses [Sphinx](https://www.sphinx-doc.org/en/master/) as its main documentation compiler. This means that the docs are kept in the same repository as the project code, and that any documentation update is done in the same way was a code contribution. ```{tip} Please notice that the [GitHub web interface](https://docs.github.com/en/repositories/working-with-files/managing-files/editing-files) provides a quick way of propose changes in `fhirpack`\'s files. While this mechanism can be tricky for normal code contributions, it works perfectly fine for contributing to the docs, and can be quite handy. If you are interested in trying this method out, please navigate to the `docs` folder in the source [repository](https://github.com/%3CUSERNAME%3E/fhirpack), find which file you would like to propose changes and click in the little pencil icon at the top, to open [GitHub\'s code editor](https://docs.github.com/en/repositories/working-with-files/managing-files/editing-files). Once you finish editing the file, please write a message in the form at the bottom of the page describing which changes have you made and what are the motivations behind them and submit your proposal. ``` When working on documentation changes in your local machine, you can compile them using `tox`\_: tox -e docs and use Python\'s built-in web server for a preview in your web browser (`http://localhost:8000`): python3 -m http.server --directory 'docs/_build/html' Code Contributions ------------------ `fhirpack` is build around the `PACK` class which uses a subclass of `pandas` `DataFrame`, called `Frame`, as the main underlying datastructure. Upon connecting to a server, the worklow follows the ETL principle. In general, methods that extract FHIR resources can be found in inside the `extraction` directory. These methods expect a list of either `fhirpy` resources, `fhirpy` references or FHIR-ID strings as input. Alternatively, the methods can operate on a `Frame` object according to the [mixin](https://www.pythontutorial.net/python-oop/python-mixin/) pattern. In this case, no other input is expected. All extraction methods return `Frame` objects which can be used by the Transformer for data manipulation or Loader for uploading. You can use Jupyter, JupyterLab or VSCode\'s Jupyter Plugin to use and improve `usage.py` and `samples.py`. However, keep in mind to not upload notebook outputs as they bloat the files and are irrelevant to the reader. To prevent that, execute: echo -e '[filter "strip-notebook-output"]\n\tclean = jupyter nbconvert \ --ClearOutputPreprocessor.enabled=True --to=notebook --stdin --stdout --log-level=ERROR' \ >> .git/config within the repository. That line defines a clean for Jupyter notebooks that git can then use for all `*.ipynb`. ### Submit an issue Before you work on any non-trivial code contribution it\'s best to first create a report in the [issue tracker](https://github.com/%3CUSERNAME%3E/fhirpack/issues) to start a discussion on the subject. This often provides additional considerations and avoids unnecessary work. ### Create an environment Before you start coding, we recommend creating an isolated [virtual environment](https://realpython.com/python-virtual-environments-a-primer/) to avoid any problems with your installed Python packages. This can easily be done via either `virtualenv`\_: virtualenv source /bin/activate or [Miniconda](https://docs.conda.io/en/latest/miniconda.html): conda create -n fhirpack python=3.9.6 six virtualenv pytest pytest-cov conda activate fhirpack or [Pipenv](https://pipenv.pypa.io/en/latest/): pipenv install fhirpack pipenv shell ### Clone the repository 1. Create an user account on GitHub if you do not already have one. 2. Fork the project [repository](https://github.com/%3CUSERNAME%3E/fhirpack): click on the *Fork* button near the top of the page. This creates a copy of the code under your account on GitHub. 3. Clone this repository to your local disk from GitHub with: git clone https://github.com/fhirpack/main.git or from GitLab with: > git clone cd fhirpack 1. You should run: pip install -U pip setuptools -e . to be able to import the package under development in the Python REPL. 2. Verify you can run tests and build `fhirpack`: tox -e; tox -e build; tox -e clean ### Dependencies This projetc relies on the followin python packages. ### Implement your changes 1. Create a branch to hold your changes: git checkout -b my-feature and start making changes. Never work on the main branch! 2. Start your work on this branch. Don\'t forget to add [docstrings](https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html) to new functions, modules and classes, especially if they are part of public APIs. 3. Test your Improvements: pytest -s --use-running-containers --docker-compose-no-build --pyargs fhirpack tests tox 4. Add yourself to the list of contributors in `AUTHORS.rst`. 5. When you're done editing, do: git add git commit to record your changes in [git](https://git-scm.com). ```{important} Don\'t forget to add unit tests and documentation in case your contribution adds an additional feature and is not just a bugfix. Moreover, writing a [descriptive commit message](https://chris.beams.io/posts/git-commit) is highly recommended. In case of doubt, you can check the commit history with: git log --graph --decorate --pretty=oneline --abbrev-commit --all to look for recurring communication patterns. ``` 6. Please check that your changes don\'t break any unit tests with: tox (after having installed `tox`\_ with `pip install tox` or `pipx`). You can also use `tox`\_ to run several other pre-configured tasks in the repository. Try `tox -av` to see a list of the available checks. ### Submit your contribution 1. If everything works fine, push your local branch to GitHub with: git push -u origin my-feature 2. Go to the web page of your fork and click \"Create pull request\" to send your changes for review. ### Troubleshooting The following tips can be used when facing problems to build or test the package: 1. Make sure to fetch all the tags from the upstream [repository](https://github.com/%3CUSERNAME%3E/fhirpack). The command `git describe --abbrev=0 --tags` should return the version you are expecting. If you are trying to run CI scripts in a fork repository, make sure to push all the tags. You can also try to remove all the egg files or the complete egg folder, i.e., `.eggs`, as well as the `*.egg-info` folders in the `src` folder or potentially in the root of your project. 2. Sometimes `tox`\_ misses out when new dependencies are added, especially to `setup.cfg` and `docs/requirements.txt`. If you find any problems with missing dependencies when running a command with `tox`\_, try to recreate the `tox` environment using the `-r` flag. For example, instead of: tox -e docs Try running: tox -r -e docs 3. Make sure to have a reliable `tox`\_ installation that uses the correct Python version (e.g., 3.7+). When in doubt you can run: tox --version # OR which tox If you have trouble and are seeing weird errors upon running `tox`\_, you can also try to create a dedicated [virtual environment](https://realpython.com/python-virtual-environments-a-primer/) with a `tox`\_ binary freshly installed. For example: virtualenv .venv source .venv/bin/activate .venv/bin/pip install tox .venv/bin/tox -e all 4. [Pytest can drop you](https://docs.pytest.org/en/stable/how-to/failures.html#using-python-library-pdb-with-pytest) in an interactive session in the case an error occurs. In order to do that you need to pass a `--pdb` option (for example by running `tox -- -k --pdb`). You can also setup breakpoints manually instead of using the `--pdb` option. Maintainer tasks ---------------- ### Releases If you are part of the group of maintainers and have correct user permissions on [PyPI](https://pypi.org/), the following steps can be used to release a new version for `fhirpack`: 1. Make sure all unit tests are successful. 2. Tag the current commit on the main branch with a release tag, e.g., `v1.2.3`. 3. Push the new tag to the upstream [repository](https://github.com/%3CUSERNAME%3E/fhirpack), e.g., `git push upstream v1.2.3` 4. Clean up the `dist` and `build` folders with `tox -e clean` (or `rm -rf dist build`) to avoid confusion with old builds and Sphinx docs. 5. Run `tox -e build` and check that the files in `dist` have the correct version (no `.dirty` or [git](https://git-scm.com) hash) according to the [git](https://git-scm.com) tag. Also check the sizes of the distributions, if they are too big (e.g., \> 500KB), unwanted clutter may have been accidentally included. 6. Run `tox -e publish -- --repository pypi` and check that everything was uploaded to [PyPI](https://pypi.org/) correctly. [^1]: Even though, these resources focus on open source projects and communities, the general ideas behind collaborating with other developers to collectively create software are general and can be applied to all sorts of environments, including private companies and proprietary code bases.